Re: [AMBER] cpptraj - atomicfluct

From: David A Case <>
Date: Mon, 15 Sep 2014 15:28:18 -0400

On Mon, Sep 15, 2014, George Tzotzos wrote:

> I’m trying to calculate B-factors for the backbone CA atoms of
> selected residues (18-125)
> My input script ( is:
> trajin
> rms first mass out rmsd_first.dat :18-125.CA
> atomicfluct out bfactor.apf @CA byatom bfactor
> Both ptraj and cpptraj produce an output (bfactor.apf) that fails to
> select the residues in the mask. Instead it produces B-factors for all
> residues (1-125).

Your mask in the atomicfluct line is ".CA", which will match all residues.
If you don't want to consider residues 1-17, then just remove them from the
output; or use the same mask in the atomicfluct command that you used in the
rms command.

You could try replacing "byatom" with "byres" if you want residue numbers;
make sure you get the same fluctuation magnitudes, just with different labels.


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Received on Mon Sep 15 2014 - 12:30:02 PDT
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